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Fix CAT_FASTQ output

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This commit is contained in:
James Fellows Yates 2022-04-08 11:58:16 +02:00
parent 7b08c49cd6
commit 74c496f6af
1 changed files with 5 additions and 2 deletions
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7
workflows/taxprofiler.nf
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@ -140,8 +140,7 @@ workflow TAXPROFILER {
} }
.groupTuple() .groupTuple()
ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat ) ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat ).reads
} else { } else {
ch_reads_runmerged = ch_shortreads_filtered ch_reads_runmerged = ch_shortreads_filtered
.mix( ch_longreads_preprocessed ) .mix( ch_longreads_preprocessed )
@ -247,6 +246,10 @@ workflow TAXPROFILER {
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions ) ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
} }
if (params.run_merging){
ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
}
if (params.run_kraken2) { if (params.run_kraken2) {
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) ) ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() ) ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )